body {
  padding-top: 70px;
}
.navbar-fixed-top {
  background-color: #9e9f9f;
}

.tip-help {
    cursor: pointer; 
}

.vertical-align {
    display: flex;
    align-items: center;
}

.row{
  margin-top: 10px;
  margin-bottom: 15px;
}

.msi_button {
    margin-bottom: 10px;
}

.ui-widget-content {
    background: none;
    border: none;
}

.ui-widget-header {
    background: rgba(255, 255, 255, 0);
    border: 1px solid rgba(195, 219, 255, 0);
}

.score-filter {
    border: 1px solid #DDD;
}

.brush .extent {
    fill-opacity: .125;
    shape-rendering: crispEdges;
}

#galaxy_save {
    background-color: #9e9f9f;
    color: #337ab7;
}

.galaxy_file {
    padding: 10px 10px 10px 10px;
    background-color: #bbbbbb;
}

.selected_file {
    background-color: #4cae4c;
}

svg {
    font: 10px sans-serif;
}

.resize path {
    fill: #666;
    fill-opacity: .8;
    stroke: #000;
    stroke-width: 1.5px;
}

path {
    fill: currentColor;
    stroke: steelblue;
    stroke-width: 1.5px;
}

.axis path,
.axis line {
    fill: none;
    stroke: #000;
    shape-rendering: crispEdges;
}

.low_score {
    color: darkblue;
}
.high_score {
    color: red;
}

.score-svg-component {
    background: rgba(195, 219, 255, 0.31);
}

.glyphicon-ok-circle {
    color: green;
}

.glyphicon-ok {
    color: green;
}

.pep_seq {
    font-family: "Courier New", Courier, monospace;
    font-size: large;
    font-weight: bold;
}

.pep_seq_selected {
    background: rgba(70, 130, 180, 0.62);
}

#selectable .ui-selecting { background: rgba(70, 130, 180, 0.62); }
#selectable .ui-selected { background: darkblue; color: white; }

.well {
    background-color: #DDDDDD;
    border: 1px solid #DDDDDD;
}

.btn-group {
    padding-bottom: 15px;
}

.p_accession {
    background-color: rgba(128, 128, 128, 0.04);
}

.prot-sequence {
    color: rgba(14, 92, 173, 0.5);
    max-height: 300px;
    overflow-y: scroll;
    overflow-x: scroll;
}

.pep-cov {
    color: rgb(14, 92, 173);
}

.pep-cov-hide {
    color: transparent;
}

.inv {
    color: transparent;
}

#mod_banner {
    font-weight: 200;
    overflow-y: scroll;
    margin-bottom: 20px
}

.baseMod {
    cursor: help;
    color: rgb(10, 173, 63);
    font-size: larger;
    text-shadow: 0 1px 0 #ccc,
    0 2px 0 #c9c9c9,
    0 3px 0 #bbb,
    0 4px 0 #b9b9b9,
    0 5px 0 #aaa,
    0 6px 1px rgba(0,0,0,.1),
    0 0 5px rgba(0,0,0,.1),
    0 1px 3px rgba(0,0,0,.3),
    0 3px 5px rgba(0,0,0,.2),
    0 5px 10px rgba(0,0,0,.25),
    0 10px 10px rgba(0,0,0,.2),
    0 20px 20px rgba(0,0,0,.15);
}

.file_picker {
    cursor: pointer;    
    padding: 2em;
}

.fdr_score {
    display: block;
    width: 400px;
    padding: 10px;
    cursor: pointer;
    background-color: #337ab7;
}

.fdr_pct_value {
    display: block;
    padding: 5px;
    cursor: pointer;
}

.detail_table_title {
    cursor: pointer;
    padding: 5px;
}

.scan-mark {
    padding: 10px;
}

.u-config {
    cursor: pointer;
}
.config-true {
    color: green;
}

.config-false {
    color: red;
}

.mod-require {
    cursor: pointer;
}

td.details-control {
    width: 20px;
    cursor: pointer;
}

.app_nav_btn {
    background-color: transparent;
    color: #337ab7;
}

.igv_track_div {
    padding: 10px;
}

.igv_load_track {
    background-color: gainsboro;
}

.fv-protein {
    cursor: pointer;
}

.fv-protein:hover {
   color: #337ab7;
}

.fv-seq {
    font-size: 1.25em;
}

.fv-entry {
    background-color: gainsboro;
    margin: 5px;
}

.filter-entry {
    padding: 5px 5px 5px 5px;
    cursor: pointer;
}

.filter-entry-selected {
    background-color: #1b6d85;
}

/**
Amino Acid  Color      Triple        Amino Acid    Color  Triple
ASP,GLU   bright red [230,10,10]     CYS,MET     yellow [230,230,0]
LYS,ARG   blue       [20,90,255]     SER,THR     orange [250,150,0]
PHE,TYR   mid blue   [50,50,170]     ASN,GLN     cyan   [0,220,220]
GLY       light grey [235,235,235]   LEU,VAL,ILE green  [15,130,15]
ALA       dark grey  [200,200,200]   TRP         pink   [180,90,180]
HIS       pale blue  [130,130,210]   PRO         flesh  [220,150,130]
*/

.amino_acid {
    fill: #feedde;
    stroke: gray;
    stroke-width: 1px;
}

.reference_mismatch {
    fill: #9c3e0d;
    stroke: #9c3e0d;
    stroke-width: 5px;
}

.align_match {
    stroke: gray;
    stroke-width: 1px;
}

.ctx {
    fill: #feedde;
    stroke: gray;
    stroke-width: 1px;
}

.asp, .glu {
    fill: rgb(230, 10, 10);
}

.lys, .arg {
    fill: rgb(20, 90, 255);
}

.phe, .tyr {
    fill: rgb(50, 50, 170);
}

.gly {
    fill: rgb(235, 235, 235);
}

.ala {
    fill: rgb(200, 200, 200);
}

.his {
    fill: rgb(130, 130, 210);
}

.cys, .met {
    fill: rgb(230, 230, 0);
}

.ser, .thr {
    fill: rgb(250, 150, 0);
}

.asn, .gln {
    fill: rgb(0, 220, 220);
}

.leu, .val, .ile {
    fill: rgb(15, 130, 15);
}

.trp {
    fill: rgb(180, 90, 180);
}

.pro {
    fill: rgb(220, 150, 130);
}

.aa_residue {
    text-shadow: 1px 1px 2px white;
    font-family: monospace;
    font-size: 18px;
    fill: black;
}

.txt_pep {
    font-family: monospace;
    font-size: 18px;
    fill: black;
}

.offset {
    font-family: monospace;
    font-size: 10px;
    fill: black;
}



.psm {
    fill: #fd8d3c;
    stroke: gray;
}

.ctx_psm {
    fill: #fd8d3c;
}

.ctx_peptide {
    fill: #fdbe85;
}

.peptide {
    fill: #fdbe85;
    stroke: gray;
}

.locator {
    stroke-width: 100%;
    stroke: #333333;
    opacity: 0.2;
}

.genome_line {
    stroke: gray;
    stroke-width: 1;
    cursor: pointer;
}

.genome_dummy {
    stroke-width: 40px;
    stroke: #a8a8a8;
    stroke-dasharray: 1,1;
}

.ptm {
    fill: #E5E7E9;
}

text.ptm {
    fill: #6E2C00;
    text-shadow: 2px 2px 3px #AEB6BF;
}

text.itraq4plex {
    fill: #884EA0;
    text-shadow: 2px 2px 3px #AEB6BF;
}

text.oxidation {
    fill: #2471A3;
    text-shadow: 2px 2px 3px #AEB6BF;
}

.mismatch {
    fill: #018571;
}

.score_line {
    fill: none;
    stroke: steelblue;
    opacity: 0.5;
    stroke-width: 4px;
    cursor: pointer;
}

.decoy_score_pct {
    fill: steelblue;
    opacity: 0.5;
    stroke: gray;
    cursor:pointer;
}

.tooltip {
    background: steelblue;
    color: white;
}

.tooltip-inner {
    background: steelblue;
    color:white;
}
